Bisulphite Sequencing of Chromatin Immunoprecipitated DNA (BisChIP-seq)

Epigenetic regulation plays a critical role in gene expression, cellular differentiation, and disease. There is a complex interplay between the different layers of epigenetic information, including DNA methylation, nucleosome positions, histone modifications, histone variants, and other important epigenetic regulators. The different modifications do not act independently of each other and their relationship plays an important role in governing the regulation of the epigenome. Of these, DNA methylation is the best-studied epigenetic modification in mammals. However, the direct relationship between DNA methylation and chromatin modifications has been difficult to unravel with existing technologies, with epigenome-wide integration studies still based on "overlaying" independent chromatin modification and DNA methylation maps. Bisulphite sequencing enables the methylation state of every cytosine residue to be analyzed across a given molecule in a strand-specific context. Here, we describe a direct approach to interrogating the DNA methylation status of specific chromatin-marked DNA, using high-throughput sequencing of bisulphite-treated chromatin immunoprecipitated DNA (BisChIP-seq). This combined approach enables the exquisite relationship between chromatin-modified DNA or transcription factor-associated DNA and the methylation state of each targeted allele to be directly interrogated. BisChIP-Seq can now be widely applied genome-wide to further understand the molecular relationship between DNA methylation and other important epigenetic regulators.